I haven't actually tried an alternate keyboard layout yet so I can't vouch for it, but Colemak seems to have the edge on Dvorak.
I also do the ls -l thing all the time and finally succumbed to just uncommenting the relevant alias in my .bash_rc. 'll' just makes it easier; I don't know why I resisted enabling the alias...
I used to average 110 wpm on Qwerty. I started at 30 wpm Colemak and reached 80 in three months. After fourish years, I'm back at 110 wpm, with no more cyst or shoulder pain.
I tried Dvorak for a week but disliked that 1) it emphasizes hand alternation (as opposed to Colemak's emphasis on finger mashes) and 2) it was so difficult to type "ls -l".